1xfp
From Proteopedia
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|PDB= 1xfp |SIZE=350|CAPTION= <scene name='initialview01'>1xfp</scene>, resolution 1.50Å | |PDB= 1xfp |SIZE=350|CAPTION= <scene name='initialview01'>1xfp</scene>, resolution 1.50Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=FMT:FORMIC ACID'>FMT</scene> | + | |LIGAND= <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene> |
| - | |ACTIVITY= [http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] | + | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </span> |
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1jtt|1JTT]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1xfp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xfp OCA], [http://www.ebi.ac.uk/pdbsum/1xfp PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1xfp RCSB]</span> | ||
}} | }} | ||
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[[Category: Vynck, S.]] | [[Category: Vynck, S.]] | ||
[[Category: Wyns, L.]] | [[Category: Wyns, L.]] | ||
| - | [[Category: FMT]] | ||
[[Category: alpha-beta othogonal bundle]] | [[Category: alpha-beta othogonal bundle]] | ||
[[Category: beta sandwich]] | [[Category: beta sandwich]] | ||
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[[Category: protein-protein heterocomplex]] | [[Category: protein-protein heterocomplex]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:49:01 2008'' |
Revision as of 21:49, 30 March 2008
| |||||||
| , resolution 1.50Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | |||||||
| Activity: | Lysozyme, with EC number 3.2.1.17 | ||||||
| Related: | 1JTT
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal structure of the CDR2 germline reversion mutant of cAb-Lys3 in complex with hen egg white lysozyme
Overview
Affinity maturation of classic antibodies supposedly proceeds through the pre-organization of the reactive germ line conformational isomer. It is less evident to foresee how this can be accomplished by camelid heavy-chain antibodies lacking light chains. Although these antibodies are subjected to somatic hypermutation, their antigen-binding fragment consists of a single domain with restricted flexibility in favor of binding energy. An antigen-binding domain derived from a dromedary heavy-chain antibody, cAb-Lys3, accumulated five amino acid substitutions in CDR1 and CDR2 upon maturation against lysozyme. Three of these residues have hydrophobic side chains, replacing serines, and participate in the hydrophobic core of the CDR1 in the mature antibody, suggesting that conformational rearrangements might occur in this loop during maturation. However, transition state analysis of the binding kinetics of mature cAb-Lys3 and germ line variants show that the maturation of this antibody relies on events late in the reaction pathway. This is reflected by a limited perturbation of k(a) and a significantly decreased k(d) upon maturation. In addition, binding reactions and the maturation event are predominantly enthalpically driven. Therefore, maturation proceeds through the increase of favorable binding interactions, or by the reduction of the enthalpic penalty for desolvation, as opposed to large entropic penalties associated with conformational changes and structural plasticity. Furthermore, the crystal structure of the mutant with a restored germ line CDR2 sequence illustrates that the matured hydrophobic core of CDR1 in cAb-Lys3 might be compensated in the germ line precursor by burying solvent molecules engaged in a stable hydrogen-bonding network with CDR1 and CDR2.
About this Structure
1XFP is a Single protein structure of sequence from Camelus dromedarius and Gallus gallus. Full crystallographic information is available from OCA.
Reference
Chemical basis for the affinity maturation of a camel single domain antibody., De Genst E, Handelberg F, Van Meirhaeghe A, Vynck S, Loris R, Wyns L, Muyldermans S, J Biol Chem. 2004 Dec 17;279(51):53593-601. Epub 2004 Sep 21. PMID:15383540
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